I believe Xournal++ will be what you are looking for (once it is out of beta).
While not open source, there's also Styluslab's Write which saves the files as svg so you can open them anywhere.
At least I haven't found it myself. I find OneNote overall worse than its "competition", but since it's one of the very few cross-platform handwriting apps, I'm still using it.
It did make a switch from iPad to Samsung Tab a breeze.
Check out the TextBundle file format.
“The TextBundle file format aims to provide a more seamless user experience when exchanging plain text files, like Markdown or Fountain, between sandboxed applications.”
A bunch of apps support it. There’s a list of the front page of the website.
We never got to a point where you would have total interoperability between ODF, DOC, DOCX, RTF, etc. I think this one is even harder. Everyone want to show of as the best/fanciest/etc. HTML + CSS + SVG + JS sounds like a combo that could do it all, but then you realize that not even all browsers render the things in the same way.
So I would say that you are right - vendor lock in.